Thymus vulgaris L. is one of the most commonly used medicinal and aromatic plants (MAPs), owing to a range of therapeutic properties of its essential oil. Plant growth, biomass yield, essential oil content and composition are influenced by chemotype, environmental conditions, cultivation techniques and vegetative development. Since in MAPs cultivation special attention is paid on high quality of raw material, the adoption of sustainable agriculture methods is of pivotal importance. Therefore, we evaluated the agronomic and qualitative performances of two Thymus vulgaris L. chemotypes, organically cultivated under the Mediterranean climate of hilly lands of central Italy for three consecutive years (2017–2019). Along the trial, total above-ground dry biomass significantly increased from the 1st to 3rd year after planting and large variations in the main biological, biometric and productive traits were observed between the two chemotypes. The ‘thymol’ chemotype EO obviously showed thymol as the major constituent (51.26–49.87%) followed by γ-terpinene and p-cymene. The ‘linalool’ chemotype EO showed high percentages of oxygenated monoterpenes (about 90%) with linalool (75%), linalyl acetate (8.15%) and b-caryophyllene (3.2%) as main constituents. This study highlighted that T. vulgaris can be successfully organically grown in the hilly lands of Tuscany, with interesting biomass and essential oil yields, even though the plants were in the initial years of crop establishment (start in 2017). The introduction of this species into organic cultivation systems could contribute to obtain high-quality raw material, as well as to enhance crop rotation diversification, which is of pivotal importance in the management of organic farms.